Originally a 47 would have had a magneto rather than a distributor. However to get to your question, the 6 volt cubs as well as all other IH, and most other brands too, were POSITIVE ground, so the negative wire would have gone to the distributor. They did not change to negative ground until they went to 12 volt electrical systems.

G'day Whilst you are awaiting your manuals, suggest you read this one : McCormick-Deering Farmall Cub Owner's Manual 5-23-47. Verifying a particular wiring situation on 2 other Farmalls does not mean that they are correct. The page you referenced clearly states a battery ignition - which means a distributor and not a magneto. I think you will find out that as John indicated it is correct especially since it should be a positive ground system.

Positive ground systems are not as familiar to many people less than a certain age or are into restoring pre 67 cars/trucks etc., As you get used to Cubs this will become more understandable.

A '47 Cub, when built, would have matched the first diagram above. When converted to battery ignition, the coil should have been connected with + connected to the distributor. The second diagram above is for a later 12-volt Cub.

The Battery Ignition Packages for Tractors describes how the Battery Ignition/distributor is installed on an Cub equipped with a Magneto. This should solve the issues. As Jim said, the latter diagram on page 9-5 is for the later 12v tractors not the 6v ones.